Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

Bertani, Iris; Abbruscato, Pamela; Piffanelli, Pietro; Subramoni, Sujatha; Venturi, Vittorio

doi:10.1111/1758-2229.12403

Cited by 79 publications

(59 citation statements)

References 31 publications

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“…Italy [15]. The abundance of Delta and Epsilonproteobacteria in the study in rice in Italy totaled 5.4…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 91%

“…First, Microvirgula aerodenitrificans, the most abundant one, is an aerobic denitrifier [60] and has been reported previously as a rice endorhizosphere inhabitant [15]. Secondly Caulobacter sp., which has also been reported to be associated rice in two other parts of the world [61][62] [15] and to have PGP properties [48]. In the endorhizosphere of the DANAC SD20A rice cultivar, strains belonging to the Azospirillum, Acinetobacter and Citrobacter genera were dominant.…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 94%

“…is a soil bacterium from the Rhizobiales family, nodule forming and nitrogen fixing [59] and has also been reported in the potato endorhizosphere [55]. Bacteria belonging to these three genera have been detected in the rice endosphere of rice grown in Italy [15].…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 97%

“…Opitutus sp. has been reported as an inhabitant of anoxic rice paddy soils [52] and as a rice endophyte [15], moreover members of Verrucomicrobiae in the rice endosphere have also been reported by [14]. Interesting Opitutus sp.…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 98%

“…have been reported as members of the rice endosphere [15], however with a lower abundance (between 0.01 and < 1 %). In addition Cellvibrio species are nitrogen fixing bacteria, especially the Cellvibrio diazotrophicus [41].…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 99%

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Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Moronta-Barrios¹,

Gionechetti²,

Pallavicini³

et al. 2017

Preprint

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Abstract:Rice is currently the most important food crop in the world and we are only just beginning to study the bacterial associated microbiome. It is of importance to perform screenings of the core rice microbiota and also to develop new plant-microbe models and simplified communities for increasing our understanding about the formation and function of its microbiome. In order to begin to address this aspect, we have performed the isolation of hundreds bacterial isolates obtained from endorhizosphere of two rice cultivars from Venezuela. The validation of plant-growth promoting bacterial activities in vitro has led us to select and characterize 15 isolates for in planta studies such as germination test, endophytism ability and plant growth promotion. Consequently, a set of 10 isolates was selected for the set-up of an endophytic consortium as a simplified model of the natural rice bacterial endomicrobiota. Upon inoculation, the colonization and abundance of each strain within the rice roots was tracked by a culture-independent technique in gnotobiotic conditions in a 30 days period. Four strains belonging to Pseudomonas, Agrobacterium and Delftia genera have shown a promising capacity for colonizing and coexistence in root tissues. On the other hand, a bacterial community taxonomic profiling of the rhizosphere and the endorhizosphere of both cultivars were obtained and are discussed. This study is part of a growing body of research on core crops microbiome and simplified microbiomes, which strengthens the formation process of the endophytic community leading to a better understanding of the rice microbiome.

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“…Italy [15]. The abundance of Delta and Epsilonproteobacteria in the study in rice in Italy totaled 5.4…”

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 91%

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 94%

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 97%

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 98%

Section: Amplicon-based Taxonomic Profilingmentioning

confidence: 99%

See 3 more Smart Citations

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Moronta-Barrios¹,

Gionechetti²,

Pallavicini³

et al. 2017

Preprint

Self Cite

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Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species, Capsella bursa‐pastoris

Choi

Jeong

Kim

2022

Ecology and Evolution

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Recent studies have revealed that some bacteria can inhabit plant seeds, and they are likely founders of the bacterial community in the rhizosphere of or inside plants at the early developmental stage. Given that the seedling establishment is a critical fitness component of weedy plant species, the effects of seed endophytic bacteria (SEB) on the seedling performance are of particular interest in weed ecology. Here, we characterized the SEB in natural populations of Capsella bursa ‐ pastoris , a model species of weed ecology. The composition of endophytic bacterial community was evaluated using deep sequencing of a 16S rDNA gene fragment. Additionally, we isolated bacterial strains from seeds and examined their plant growth‐promoting traits. Actinobacteria, Firmicutes, Alpha‐, and Gammaproteobacteria were major bacterial phyla inside seeds. C . bursa ‐ pastoris natural populations exhibited variable seed microbiome such that the proportion of Actinobacteria and Alphaproteobacteria differed among populations, and 60 out of 82 OTUs occurred only in a single population. Thirteen cultivable bacterial species in six genera ( Bacillus , Rhodococcus , Streptomyces , Staphylococcus , Paenibacillus , Pseudomonas ) were isolated, and none of them except Staphylococcus haemolyticus were previously reported as seed endophytes. Eight isolates exhibited plant growth‐promoting traits like phosphate solubilization activity, indole‐3‐acetic acid, or siderophore production. Despite the differences in the bacterial communities among plant populations, at least one isolated strain from each population stimulated shoot growth of either C . bursa ‐ pastoris or its close relative A . thaliana when grown with plants in the same media. These results suggest that a weedy plant species, C . bursa ‐ pastoris , contains bacterial endophytes inside their seeds, stimulating seedling growth and thereby potentially affecting seedling establishment.

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Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

et al. 2021

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The multi‐domain bacterial S1 protein is the largest and most functionally important ribosomal protein of the 30S subunit, which interacts with both mRNA and proteins. The family of ribosomal S1 proteins differs in the classical sense from a protein with tandem repeats and has a “bead‐on‐string” organization, where each repeat is folded into a globular domain. Based on our recent data, the study of evolutionary relationships for the bacterial phyla will provide evidence for one of the proposed theories of the evolutionary development of proteins with structural repeats: from multiple repeats of assembles to single repeats, or vice versa. In this comparative analysis of 1333 S1 sequences that were identified in 24 different phyla, we demonstrate how such phyla can form independently/dependently during evolution. To the best of our knowledge, this work is the first study of the evolutionary history of bacterial ribosomal S1 proteins. The collected and structured data can be useful to computer biologists as a resource for determining percent identity, amino acid composition and logo motifs, as well as dN/dS ratio in bacterial S1 protein. The obtained research data indicate that the evolutionary development of bacterial ribosomal S1 proteins evolved from multiple assemblies to single repeat. The presented data are integrated into the server, which can be accessed at http://oka.protres.ru:4200.

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Rice bacterial endophytes: isolation of a collection, identification of beneficial strains and microbiome analysis

Cited by 79 publications

References 31 publications

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Isolation and Studies on Bacterial Endophytes from Two Venezuelan Rice Cultivars

Variation of the seed endophytic bacteria among plant populations and their plant growth‐promoting activities in a wild mustard plant species, Capsella bursa‐pastoris

Sequence and evolutionary analysis of bacterial ribosomal S1 proteins

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